Assign RSID to ID . / blank column in vcf file

Question

[Nai]

I have vcf file which ID column has input: "." output: chr1:82154 or rs4477212. I am doing using bcftools with the command:

bcftools annotate -a All_SNP.vcf.gz -c ID -o File.vcf.gz input.vcf.gz

Because All_SNP.vcf.gz has chr information as numeric while input.vcf has chr1.

I tried with snpsift tool which is not doing in correct manner, generated file lost some columns.

[Pierre Lindenbaum]

has chr information as numeric while input.vcf has chr1.

VCF files: Change Chromosome Notation ; Rename Chromosome position/Notation in VCF file ; ....